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Officials from the breakaway region's Interior Ministry on April 25 said a grenade launcher hit the building in Tiraspol. The ministry said on Facebook that some of the building's windows were broken and that smoke poured from the structure.
There has been no claim of responsibility for the incident and no reports of casualties.
The Intelligence Directorate of the Ukrainian Defense Ministry responded to the attack in a statement, saying it was "one of a number of provocative measures organized by the FSB to instill panic and anti-Ukrainian sentiment."
The Intelligence Directorate's statement said the building was damaged and windows were broken, but it said the incident came as no surprise to the leadership of the separatists.
It quoted information in a letter dated April 22 from Vadym Shmalenko, secretary of the State Commission for Emergency Situations of the Transdniester region, to the head of the Kamensky district, Volodymyr Bychkov, about the need to prepare.
"That is, three days before the incident [separatist leaders] were already preparing for it and took care of the installation of a secure and comfortable bunker," the Intelligence Directorate said.
According to the authors of the letter, the separatist leaders "should justify the war on the territory of Ukraine or involve the Transdniester region in hostilities either as a territory with a certain mobilization reserve or as a territory from which Russian troops can carry out attacks on Ukrainian territory," it said.
The directorate published what it said was a copy of the April 22 letter, whose authenticity could not be verified.
It pointed out that on the same day the acting commander of Russia's Central Military District, Rustam Minnekayev said that Russian forces aimed to take full control of southern Ukraine, saying such a move would also open a land corridor to Transdniester.
Moldova's Office for Reintegration Policy said it was "concerned," adding that it believes that the incident "is related to the creation of pretexts for the tension in the security situation in the Transdniester region, which is not controlled by the constitutional authorities."
It called for calm and for "competent national institutions" to monitor the situation.
The Moldovan Intelligence and Security Service (SIS) met in an emergency meeting in Chisinau, TV8 reports. SIS Director Alexandru Esaulenco was quoted as saying the service was collecting information.
The incident came hours after Deputy Foreign Minister Andrei Rudenko said in Moscow that Russia saw no risk to its citizens in Transdniester.
"Our position remains the same: We are calling for a peaceful settlement of the Transdniester issue while respecting Moldova's territorial integrity and a special status for this region," Rudenko was quoted as saying by Interfax.
Moldova, which borders on Ukraine, lost effective control over Transdniester after breakaway leaders declared independence in 1990.
That declaration has not been recognized by any UN member state.
But it sparked a war in 1992 between Moldova and rebels in Transdniester backed by Russia over the narrow strip of land between the Dniester River and the Ukrainian border.
Russia still has around 1,400 troops stationed in Transdniester.
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